Not to get into the wisdom, desirability, or validity of software patents; also here's the obligatory "IANAL" disclaimer . . .

No license is going to magically make something which infringes on someone's patent not infringe. Licensing might affect the degree that the patent owner can go after users of the infringing code (i.e. the infringer has promised to indemnify them against litigation, but they're still on the hook) but that's about it I believe.

Now the situation of the infringement might make a difference in the remedy imposed. One could imagine Random Megacorp willfully infringing and profiting from J Random Smallbiznezzman's patent being treated more harshly than J Random Student who published an open source program as part of his graduate work which happened to implement a patented algorithm.

If you're really interested, I've been pointed at Web & Software Development: A Legal Guide ISBN 1413300871 as a good resource; I'm perpetually pointing people at it and perpetually leaving it in my Amazon wish list, but Nolo is a respected source for legal guides and information (and you may find more information there; they have a section specifically on patent law).

Update: I just recalled seeing something from /. on M$ licensing any potential patents in Linux to Novel that there's talk about the GPL3 making distributing GPL'd code implicitly grant a license to patents held by the distributers or some such (it's not exactly clear from that article). But this would seem to require the patent owner to be using some GPL'd software, so I don't know if that's what the OP was asking or not.